This is a demonstration environment. It may contain non-accurate test data and should not be used for real-world applications. Data will be deleted regularly.

LOC_000P34A.1

Display Name: Pakistan/LOC_000P34A.1/2019
Umair, M.; Rehman, Z.; Whitmer, S.; Mobley, M.; Fahim, A.; Ikram, A.; Salman, M.; Montgomery, J. M.; Klena, J. D.; Khurshid, A.; Talundzic, E.; Montgomery, J.; Klena, J.

Submission details

Submission ID
OM162075.1.S
Submitting group
Automated Ingest from INSDC/NCBI Virus by Loculus
Date submitted
2025-03-11 18:18:53 UTC
Date released
2025-03-11 18:22:52 UTC

Data use terms

Data use terms
OPEN

Data Use Terms History

ChangedUserData Use Terms
2025-03-11 18:18insdc_ingest_userOPEN
Data use terms URL
https://#TODO-MVP/open

Authors

Author affiliations
CDC, NCEZID-VSPB

Alignment and QC metrics S

Completeness S
93.12%
Length S
1557
Total ambiguous nucs S
0
Total deleted nucs S
2
Total frame shifts S
0
Total inserted nucs S
2
Total SNPs S
201
Total unknown nucs S
0

Sample details

Earliest release date
2024-07-26
Collection country
Pakistan
Collection date
2019
Collection date (lower bound)
2019-01-01
Collection date (upper bound)
2019-12-31
Isolate name
202000287_922019|Pakistan|2019

Host

Host name scientific
Homo sapiens
Host taxon id
9606

INSDC

INSDC accession S
OM162075.1
NCBI release date
2024-07-26

Nucleotide mutations

Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

Substitutions

S

  • S:A50G
  • S:G54A
  • S:G76A
  • S:T79C
  • S:A85G
  • S:T88C
  • S:G91A
  • S:T106C
  • S:A109G
  • S:A118G
  • S:A121G
  • S:C142A
  • S:T144A
  • S:C145T
  • S:A148G
  • S:C166T
  • S:G169A
  • S:G171A
    • Deletions
    S:1531, S:1532
    Insertions
    ins_S:1536:A, ins_S:1540:T

    Amino acid mutations

    Mutations called relative to the NC_005301.3, NC_005300.2 & NC_005302.1 references

    Substitutions

    NP

  • NP:F30Y
  • NP:S39N
  • NP:V83A
  • NP:D116E
  • NP:T124S
  • NP:G125N
  • NP:H195R
  • NP:D199E
  • NP:I246V
  • NP:S301G
  • NP:A307V
  • NP:P321S
  • NP:E322D
  • NP:Q405L
  • NP:E421D
  • NP:V436I
    • Deletions
    None
    Insertions
    None

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